[Mristudio-users] more DiffeoMap questions

[Varin Tsai]

Hi,

I have a question on file conversion and Siemens Mosaic files.  I 
recently received a patient for processing whos files came in Siemens 
Mosaic.  After having ran through such protocols as DCM2NII.gui, I had a 
30 direction set of files that, when run through Diffusion 
Toolkit/Trackvis, yielded me a 6x6 matrix view of the transaxial cuts of 
the brain.  I ran this through DTI studios because of its actual Siemens 
Mosaic protocol and was able to (with the right gradient table) create a 
semi-usable FA map.  The problem is that while DTI studios gave me a 
representation of the brain, the coronal and sagittal views are 
upside-down and inverted.  I'd like to know if anybody had thoughts on 
reorienting those views of the brain.

I had tried going through Vinci 2.54.0 to use Magic Tool (for those not 
acquainted, Magic Tool allows you to tilt and rotate images how you 
please in order for them to fit your needs), however if I try to rotate 
the sagittal cut, the rest of the cuts are affected such that the 
transaxial cut will be flipped - they are, as expected, linked.

If anyone could provide any insight on either using DTI studios to 
correctly convert the Siemens Mosaic files into usable directions for 
tractography purposes (either in DTI studios or Diffusion 
Toolkit/Trackvis), I'd greatly appreciate it.  Thanks!

Varin Tsai

On 1/14/2011 10:51 AM, Sourena Soheili wrote:
> Dear Mojdeh
> Are you iranian? Cuz I'd like to find someone with my nationality here
> for consult.
> Sourena
>
> On Thursday, January 6, 2011, Mojdeh<zamyadim at sri.utoronto.ca>  wrote:
>> Hi all :)
>> I finally managed to successfully run and download the results of my
>> first LDDMM job ... now I have a question about viewing the output
>> transformations. In the manual located @
>> https://www.mristudio.org/wiki/user_manual/diffeomap/MultichannelVolumeLDDMM
>> , it's mentioned that "output transformation matrix can be loaded by
>> clicking the load button under the Volume LDDMM menu and can be saved
>> Raw format. However, in my DiffeoMap there is only one "Retrieve Results
>> > From Remote Volume LDDMM" which can only be used for retrieving the data
>> and not loading them! Could you please advise me on how to access the
>> raw transformations and also how to view the "transformed target" image?
>> Thanks for the help,
>> Mojdeh
>>
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